Software Updates

ORCA

an electronic structure program package that is a flexible, efficient, and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules.

REFMAC

carries out rigid body, tls, restrained or unrestrained refinement against Xray data, or idealisation of a macromolecular structure. It minimises the coordinate parameters to satisfy either a Maximum Likelihood or Least Squares residual. REFMAC also produces an MTZ output file containing weighted coefficients for SigmaA weighted mFo-DFcalc and 2mFo-DFcalc maps, where missing data have been restored.

SCIPION

an image processing framework to obtain 3D models of macromolecular complexes using 3D EM that allows you to execute workflows combining different software tools, while taking care of formats and conversions.

SPHIRE

(SParx for HIgh Resolution Electron microscopy) for cryoEM using statistical resampling to attain quality assessment and result reproducibility. Includes movie frame alignments (movie), CTF estimation of raw electron micrographs (cter), picking/stack creation (window), reproducible 2-D classification (isac), reproducible initial model generation (viper), automatic gold-standard 3-D refinement (meridien), local resolution estimation and filtering (localres), and up to the 3-D sorting of different conformational states based on the statistical 3-D variability of the data (sort3D).

IMOD

a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections.

DIALS

(Diffraction Integration for Advanced Light Sources) a software project for the analysis of crystallographic diffraction images for many new methods from shutterless, fine-sliced rotation scans to randomly-oriented snapshots of serial crystallography. It uses multiple CPU and GPU machines to increase speed and accuracy based on a comprehensive physical model.

CAVER Analyst

a software tool for the calculation, analysis, and real-time visualization of access tunnels and channels in static and dynamic protein structures with an intuitive GUI.

HHsuite

an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).